Javier and Mark, Thank you SO much! That is so helpful to me.
If you have time, I have two follow-up questions: (1) From your answer, it seems that in OPLS, 1-4 interactions will be taken into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified in [ pairs ], even if gen-pairs = yes and sigma and epsilon values are provided in [ atomtypes ] in ffnonbonded.itp. But what about 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions, in a protein for example? I think that in OPLS, such interactions are to be considered at full strength (no scaling down). My question is: are these 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions automatically taken into account if gen-pairs = yes? (2) Suppose that I run grompp (where 1-4 interactions are specified in [ pairs ] and gen-pairs = yes) and grompp gives me the following output: Generated 276 of the 276 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 276 of the 276 1-4 parameter combinations Does this output indeed imply that the ONLY nonbonded interactions considered are 1-4 interactions? In other words, does this output suggest that NO 1-5, 1-6, 1-7, ..., 1-Infinity nonbonded interactions are considered? If so, why is this the case if I have set gen-pairs = yes? Andrew DeYoung Carnegie Mellon University -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
